Fix PDB molecule for animations

docs/tutorials/atomic_blender/fix_pdb_model.md

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+---
+layout: default
+title: Fix a PDB Model
+parent: Atomic Blender
+nav_order: 2
+---
+
+## LOAD A PDB FILE
+
+### Setup
+
+ * Blender version 4.0
+ * Blender empty file
+
+### PDB MOLECULE
+
+Got a structure of ciprofloxacin in SDF format from here: 
+
+https://www.molinstincts.com/sdf-mol-file/ciprofloxacin-sdf-CT1000048109.html
+
+translated to PDB with: 
+
+https://datascience.unm.edu/tomcat/biocomp/convert (3D)
+
+Sometimes you get DivisionByZero, try to use a different converter.
+
+### WORKFLOW
+
+1. Delete the cube with `X`
+2. Import file [Ciprofloxacin](https://raw.githubusercontent.com/tucano/blender4science/main/course_material/Atomic_Blender/02_fix_pdb/ciprofloxacin.pdb)
+
+3. Import Settings:
+
+    | Parameter     | Value      |
+    |:--------------|:-----------|
+    | Balls type    | Mesh       |
+    | Balls radius  | 0.5        |
+    | Stick type    | Duplivert  |
+    | Bonds         | Active     |
+    | Bond radius   | 0.1        |
+
+4. Now we are going to merge all atoms and sticks to create a unique mesh. We will work in the Outlier
+5. Select Hydrogen and hide it, notice that the sticks are closed. 
+6. Remove the cups just deleting the underling model (Hydrogen_sticks_cup)
+7. Do the same for all sticks: extra faces will interfere with shading.
+8. Convert the instance of Carbon_Stick_mesh to a real mesh: `CTRL-A` and make instance real.
+9. Select an active stick with `CTRL-Click` and `CTRL-J` to join segments
+10. `TAB` to enter edit mode and than `M` and merge by distance to cleanup vertices
+11. Do this tedious thing for all the sticks, remember to go back in object mode.
+12. Join all sticks in a single mesh: select in outlier and `CTRL-J` and rename it `sticks`
+13. On Outlier, create a new collection under Scene collection (name: 'Molecule')
+14. In Outlier move the sticks object to the new collection
+15. Do the same with atoms:
+    - `CTRL-A` make instance real
+    - `CTRL-Click` and select one atom
+    - `CTRL-J` and join all
+    - `TAB` and `M` to merge by distance
+16. Merge all atoms together with `CRTL-J`
+17. Named it balls and move to the collection `Molecule`
+18. Select balls: In the Material properties you notice there are multiple materials: rename them as XXX.Atoms (example: Carbon.Atoms)
+19. Now we want to separate the bonds and atoms materials. Select sticks and make new materials called XXX.Bonds
+20. We can now merge sticks and balls with `CTRL-J`
+21. Rename final mesh `Ciprofloxacin`
+22. Now that we have a single molecule we can do a lot of cool things! For example let's WAVE this molecule for no reason!
+23. On Modifiers add a Wave modifier, play animation and see your molecule waving!
+24. Add a rotating animation: 
+    - Remove the wave
+    - `N` for item properties
+    - `I` overing 'Rotation' to insert a keyframe
+    - Go to frame 100
+    - Rotate 360 on Z axis with `RZ360`
+    - Go to frame 120
+    - Rotate again on Z axis 360
+25. Render animation (EEVE)